Tool: gprofileR

net_dir = "/pastel/projects/speakeasy_dlpfc/SpeakEasy_net_MF/"
modules_file = read.table(paste0(net_dir, "geneBycluster.txt"), header = T)

Enrichment Level 03

We removed the clusters with < 30 nodes for downstream analysis.

modules_file = modules_file[, c("symbol", "cluster_lv3")]
modules_file$module_clusters = paste0("m", modules_file$cluster_lv3)
modules_file$cluster_lv3 = NULL

modules_size = as.data.frame(table(modules_file$module_clusters))
colnames(modules_size) = c("module", "n_nodes")
createDT(modules_size)

Module enrichment L3

Module m5

Module m23

Module m36

Module m12

Module m8

Module m41

Module m40

Module m4

Module m31

Module m11

Module m35

Module m7

Module m32

Module m1

Module m26

Module m28

Module m2

Module m3

Module m27

Module m29

Module m45

Module m9

Module m42

Module m24

Module m46

Module m37

Module m30

Module m44

Module m25

Module m6

Module m13

Module m43

Module m10

Module m33

Session info

sessionInfo()

R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] DT_0.20 plotly_4.10.0 ggplot2_3.3.5 knitr_1.37
[5] gprofiler2_0.2.1

loaded via a namespace (and not attached): [1] tidyselect_1.1.2 xfun_0.29 bslib_0.3.1 purrr_0.3.4
[5] colorspace_2.0-3 vctrs_0.3.8 generics_0.1.2 htmltools_0.5.2
[9] viridisLite_0.4.0 yaml_2.3.5 utf8_1.2.2 rlang_1.0.1
[13] later_1.3.0 jquerylib_0.1.4 pillar_1.7.0 glue_1.6.1
[17] withr_2.4.3 DBI_1.1.2 lifecycle_1.0.1 stringr_1.4.0
[21] munsell_0.5.0 gtable_0.3.0 htmlwidgets_1.5.4 evaluate_0.15
[25] fastmap_1.1.0 httpuv_1.6.5 crosstalk_1.2.0 fansi_1.0.2
[29] Rcpp_1.0.8 xtable_1.8-4 promises_1.2.0.1 scales_1.1.1
[33] jsonlite_1.7.3 mime_0.12 digest_0.6.29 stringi_1.7.6
[37] shiny_1.7.1 dplyr_1.0.8 grid_4.1.2 cli_3.2.0
[41] tools_4.1.2 bitops_1.0-7 magrittr_2.0.2 sass_0.4.0
[45] lazyeval_0.2.2 RCurl_1.98-1.6 tibble_3.1.6 crayon_1.5.0
[49] tidyr_1.2.0 pkgconfig_2.0.3 ellipsis_0.3.2 data.table_1.14.2 [53] assertthat_0.2.1 rmarkdown_2.11 httr_1.4.2 rstudioapi_0.13
[57] R6_2.5.1 compiler_4.1.2